[gmx-users] pair distribution function

[Archana Sonawani-Jagtap]

Thank you.


On Sun, Oct 6, 2013 at 8:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote:
>
>> I have simulations for different peptides in POPC bilayer.
>>
>> I want to calculate pair distribution function (pdf) between negatively
>> charged phosphate residue of POPC and positively charged residues of
>> peptide. Is there any tool available in gromacs for plotting these values?
>>
>>
> The closest you can get with a built-in Gromacs program is a radial
> distribution function with g_rdf.
>
>
>  Secondly, how to calculate the center of mass for a bilayer?
>>
>>
> g_traj -ox -com
>
> -Justin
>
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-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339